Deep geological disposal of high level radioactive waste is considered to be more stable and safer way to isolate high level radioactive waste from human environment Normally, the surrounding rock is expected to be low permeable matrix. The safety of geological disposal depends on the screen effect of surrounding rock and flow with nuclear waste transport through complex fractured rocks.Therefore, it is very important to conduct hydrogeological assessment at potential disposal sites of interest.Yamansu and Tianhu area, the important potential area for China’s high level radioactive waste repository, is located in Xinjiang Uigur municipality, northwesten China. Granite is the host rock of the repository. During last 3 years, the regional hydrogeological investigations were carried out. Based on the field investigation and sample measurement, this paper mainly studied the isotopic characteristics and its hydrogeological significance in the area. The results show that the δ2H values of shallow groundwaters are generally from 10.6‰ to -82.5‰ with mean value of -46.1‰ and theδ18O values are mostly in the range of 10.2‰ to -9.8‰ ‰ with mean value of -2.06‰ The tritium content of groundwater is from ＜1TU to 46.1TU. From the plot of δ2H versus δ18O, it can be found that stable hydrogen and oxygen isotopic compositions of the groundwater falls on a line near or lower to that of world meteoric water line, indicating that the shallow groundwater is of modern meteoric origin and recharged by recent and local precipitation, and affected intensively by evaporation. In addition, through comparison of the isotope compositions between groundwater and surface water, it can be seen both of them are very close further indicating the groundwater is mainly recharged by recent and local precipitation. The renewal ability of deep groundwater is clearly weaker than that of shallow groundwater. This cognition provided very important hydrogeological evidences for site selection and evaluationin the area.